Detail Information

Publications41

Ryan K ShultzabergerDepartment of Molecular and Cell Biology, University of California, Berkeley, United States of AmericaPLoS ONE 2:e1199. 2007

..Interestingly, we found that the major determinant of Met4 regulation was the sum of the strength of the Cbf1 and Met31 binding sites and that the energetic costs associated with spacing appeared to be minimal...

Emily E HareDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of AmericaPLoS Genet 4:e1000106. 2008

..Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function...

..Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa...

..We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors...

..We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstream of each gene's translation start site (the upstream control region (UCR))...

..We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt...

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting

Daniel A PollardGraduate Group in Biophysics, University of California Berkeley, Berkeley, California, USAPLoS Genet 2:e173. 2006

..Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics...

Alan M MosesGraduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of AmericaPLoS Comput Biol 2:e130. 2006

..Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements...

Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase

..These mechanisms are likely involved in the etiology of Cornelia de Lange syndrome, in which mutation of one copy of the NIPBL gene encoding the human Nipped-B ortholog causes diverse structural and mental birth defects...